Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
AFF1

Cell type

Cell type Class
Digestive tract
Cell type
DLD-1
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
DLD-1
cell line
Colorectal adenocarcinoma DLD-1
genotype
AFF1-AID OsTIR1
chip antibody
AF4 Bethyl A302-345A

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen). For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 or NovaSeq 6000 (Illumina).

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
25886712
Reads aligned (%)
93.6
Duplicates removed (%)
5.3
Number of peaks
791 (qval < 1E-05)

hg19

Number of total reads
25886712
Reads aligned (%)
92.9
Duplicates removed (%)
6.3
Number of peaks
945 (qval < 1E-05)

Base call quality data from DBCLS SRA